One thought from justins post in the past, Look at the .trj in VMD with the unit cell box and see if something sticks out at the end (ie comes up in the bootmn of the box from the top). It then does what you show, however it may not be that. If it is, you'll have to increase your box deminsion in the pull dir. and re-run it or throw out the data after it turns negative...
Steve -------- Original-Nachricht -------- > Datum: Wed, 16 May 2012 10:08:06 +0200 > Von: "Du Jiangfeng (BIOCH)" <j...@maastrichtuniversity.nl> > An: "gmx-users@gromacs.org" <gmx-users@gromacs.org> > Betreff: [gmx-users] Wierd results from Umbrella sampling > Dear Sir/Madam, > > I have performed umbrella pulling and umbrella sampling my protein from a > DOPC/DOPS membrane. Unfortunately, the results are really bad (Energy curve > suddenly turns to zero at the last 1 nm) and the histograph does not show > any overlap. Actually, I did it strictly based on Justin's tutorial, with > the sample spacing of 0.2 nm. > > Here are some lines from the end of the energy file (The energy should not > decrease since it was in summation): > > Distance(nm) Energy (Kcal/mol) > 5.288348 5.705318e+01 > 5.316250 4.881724e+01 > 5.344152 4.022505e+01 > 5.372054 3.101854e+01 > 5.399956 2.208200e+01 > 5.427858 1.343340e+01 > 5.455761 4.267619e+00 > 5.483663 -5.084078e+00 ? minus > 5.511565 -1.486168e+01 ? minus > 5.539467 -2.393515e+01 ? minus > 5.567369 -3.343453e+01 ? minus > > > Followings are some lines from the end of histograph file: > > Distance(nm) > 5.455761 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 8 > 5.483663 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 8 > 5.511565 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 12 > 5.539467 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 4 > 5.567369 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 2 > > > I am really depressed because it took me quiet a long time to sampling but > it seems in vain... I really no idea to find out what went wrong. > > I am looking forward to your help. Thanks a lot. > > Jiangfeng. > > > > > Jiangfeng Du, PhD Student > Cardiovascular Research Institute Maastricht > Department of Biochemistry > P.O. Box 616 > Mobile: +31-681741859 > FAX: +31-43-3884159 > 6200 MD Maastricht > The Netherlands-- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
